Self-assembly of molecules and colloids

The design of building blocks programmed to self-assemble desired materials is a grand challenge in materials science. We have coupled molecular simulation, statistical thermodynamics, and machine learning to expose the relationship between building block chemistry and architecture and the morphology and properties of the resulting self-assembled aggregates. We have used these learned relations to understand and perform inverse design in a number of substrates including pi-conjugated peptides, peptoids, colloids, nanoparticles, and nucleic acids.

We are pursuing the following projects in this theme:

  • High-throughput virtual screening of sequence-defined peptoids to assemble around metal clusters
  • Data-driven control of optically-bound nanoparticles
  • Theoretical understanding of peptoid supramolecular assembly into sheets and nanotubes
  • Sequence-defined kinetics of nucleic acid assembly

Representative Publications

105.   M. Zhao, S. Zhang, R. Zheng, S. Alamdari, C.J. Mundy, J. Pfaendtner, L.D. Pozzo, C.-L. Chen, J. DeYoreo, and A.L. Ferguson* “Computational and experimental determination of the properties, structure, and stability of peptoid nanosheets and nanotubes” Biomacromolecules (in press, 2023) [ https://doi.org/10.1021/acs.biomac.3c00107 ]

102.  B. Ashwood, M.S. Jones, A.L. Ferguson, and A. Tokmakoff “Disruption of energetic and dynamic base pairing cooperativity in DNA duplexes by an abasic site” Proc. Natl. Acad. Sci. USA 120 14 e2219124120 (2023) [ https://doi.org/10.1073/pnas.2219124120 ]

99.     Y. Ma, R. Kapoor, B. Sharma, A.P. Liu, and A.L. Ferguson* “Computational design of self-assembling peptide chassis materials for synthetic cells” Mol. Syst. Des. Eng. 8 39-52 (2023) [ https://dx.doi.org/10.1039/D2ME00169A ]

95.     S. Chen, J.A. Parker, C.W. Peterson, S.A. Rice, N.F. Scherer, and A.L. Ferguson* “Understanding and design of non-conservative optical matter systems using Markov state models” Mol. Sys. Des. Eng. 7 1228-1238 (2022) [ http://dx.doi.org/10.1039/D2ME00087C ]

94.     K. Shmilovich, S.S. Panda, A. Stouffer, J.D. Tovar, and A.L. Ferguson* “Hybrid computational-experimental data-driven design of self-assembling π-conjugated peptides” Digital Discovery 1 448-462 (2022) [ https://dx.doi.org/10.1039/d1dd00047k ]

92.     K. Shmilovich, Y. Yao, J.D. Tovar, H.E. Katz, A. Schleife, and A.L. Ferguson* “Computational discovery of high charge mobility self-assembling π-conjugated peptides” Mol. Syst. Des. Eng. 7 447-459 (2022) [ http://dx.doi.org/10.1039/D2ME00017B ]

→ Selected by editors as MSDE HOT article

90.    S. Dasetty, I. Coropceanu, J. Porter, J. Li, J.J. de Pablo, D. Talapin, and A.L. Ferguson* “Active learning of polarizable nanoparticle phase diagrams for the guided design of triggerable self-assembling superlattices” Mol. Syst. Des. Eng. 7 350 – 363 (2022) [ http://dx.doi.org/10.1039/D1ME00187F ]

→ Selected by editors as MSDE HOT article

89.     M. Zhao, K.J. Lachowski, S. Alamdari, J. Sampath, P. Mu, C.J. Mundy, J. Pfaendtner, C.-L. Chen, L.D. Pozzo, and A.L. Ferguson* “Hierarchical self-assembly pathways of polypeptoid helices and sheets” Biomacromolecules 23 3 992-1008 (2022) [ https://doi.org/10.1021/acs.biomac.1c01385 ]

88.    B. Sharma, Y. Ma, H.L. Hiraki, B.M. Baker, A.L. Ferguson, and A.P. Liu “Facile formation of giant elastin-like polypeptide vesicles as synthetic cells” Chem. Commun. 57 13202-13205 (2021)
[ https://doi.org/10.1039/D1CC05579H ]

87.     M.S. Jones, B. Ashwood, A. Tokmakoff, and A.L. Ferguson* “Determining sequence-dependent DNA oligonucleotide hybridization and dehybridization mechanisms using coarse-grained molecular simulation, Markov state models, and infrared spectroscopy” J. Am. Chem. Soc. 143 17395-17411 (2021) [ https://doi.org/10.1021/jacs.1c05219 ]

86.     S.S. Panda, K. Shmilovich, S.M. Herringer, N.J. Marin, A.L. Ferguson, and J.D. Tovar “Computationally guided tuning of peptide-conjugated perylene diimide self-assembly” Langmuir 37 28 8594-8606 (2021) [ https://doi.org/10.1021/acs.langmuir.1c01213 ]

85.     W. Alvarado, J. Moller, A.L. Ferguson*, and J.J. de Pablo “Tetranucleosome interactions drive chromatin folding” ACS Cent. Sci. 7 6 1019–1027 (2021) [ https://doi.org/10.1021/acscentsci.1c00085 ]

→ Selected for supplementary cover art of ACS Cent. Sci. vol. 7, issue 6 (June 23, 2021)

82.     Y. Ma, J. Aulicino, and A.L. Ferguson* “Inverse design of self-assembling diamond photonic lattices from anisotropic colloidal clusters” J. Phys. Chem B 125 9 2398-2410 (2021) [ https://dx.doi.org/10.1021/acs.jpcb.0c08723 ]

→ Invited article for “Carol K. Hall Festschrift”

76.     B. Sharma, Y. Ma, A.L. Ferguson*, and A.P. Liu “In search of a novel chassis material for synthetic cells: Emergence of synthetic peptide compartment” Soft Matter 16 10769 (2020)
[ https://dx.doi.org/10.1039/D0SM01644F ]

71.      S. Panda, K. Shmilovich, A.L. Ferguson, and J.D. Tovar “Computationally guided tuning of amino acid configuration influences the chiroptical properties of supramolecular peptide-π-peptide nanostructures” Langmuir 36 24 6782–6792 (2020) [ https://dx.doi.org/10.1021/acs.langmuir.0c00961 ]

69.     E. Jira, K. Shmilovich, T. Kale, A.L. Ferguson, J.D. Tovar, and C. Schroeder “Effect of core oligomer length on the phase behavior and assembly of π-conjugated peptides” ACS Appl. Mater. Interfaces 12 20722-20732 (2020) [ https://dx.doi.org/10.1021/acsami.0c02095 ]

68.     K. Shmilovich, R.A. Mansbach, H. Sidky, O.E. Dunne, S.S. Panda, J.D. Tovar, and A.L. Ferguson* “Discovery of self-assembling π-conjugated peptides by active learning-directed coarse-grained molecular simulation” J. Phys. Chem. B 124 3873-3891 (2020) [ https://doi.org/10.1021/acs.jpcb.0c00708 ]

→ Invited submission to the “Machine Learning in Physical Chemistry” special issue
→ Selected as ACS Editors’ Choice article (March 30, 2020)
→ Selected for front cover art of JPCB vol. 124, issue 19 (May 14, 2020)

64.     B.A. Thurston, E.P. Shapera, J.D. Tovar, A. Schleife, and A.L. Ferguson* “Revealing the sequence-structure-electronic property relation of self-assembling π-conjugated oligopeptides by molecular and quantum mechanical modeling” Langmuir 35 47 15221-15231 (2019) [ https://doi.org/10.1021/acs.langmuir.9b02593 ]

63.     S. Panda, K. Shmilovich, A.L. Ferguson*, and J.D. Tovar “Controlling supramolecular chirality in peptide-π-peptide networks by variation of alkyl spacer length” Langmuir 35 43 14060-14073 (2019)
[ https://doi.org/10.1021/acs.langmuir.9b02683 ]

59.     Y. Ma and A.L. Ferguson* “Inverse design of self-assembling colloidal crystals with omnidirectional photonic bandgaps” Soft Matter 15 8808-8826 (2019) [ https://doi.org/10.1039/C9SM01500K ]

54.     A.W. Long and A.L. Ferguson* “Landmark diffusion maps (L-dMaps): Accelerated manifold learning out-of-sample extension” Appl. Comput. Harmon. Anal. 47 1 190-211 (2019)
[ http://dx.doi.org/10.1016/j.acha.2017.08.004 ]

48.     R.A. Mansbach and A.L. Ferguson* “A patchy particle model of the hierarchical self-assembly of π-conjugated optoelectronic peptides” J. Phys. Chem. B 122 44 10219-10236 (2018)
[ https://doi.org/10.1021/acs.jpcb.8b05781 ]

47.     B.A. Thurston and A.L. Ferguson* “Machine learning and molecular design of self-assembling π-conjugated oligopeptides” Mol. Sim. 44 11 930-945 (2018) [ https://doi.org/10.1080/08927022.2018.1469754 ]

46. J. Wang, M. Gayatri, and A.L. Ferguson* “Coarse-grained molecular simulation and nonlinear manifold learning of archipelago asphaltene aggregation and folding” J. Phys. Chem. B 122 25 6627-6647 (2018)
[ https://doi.org/10.1021/acs.jpcb.8b01634 ]

45.     L. Valverde, B.A. Thurston, A.L. Ferguson, and W.L. Wilson “Evidence for prenucleated fibrilogenesis of acid-mediated self-assembling oligopeptides via molecular simulation and fluorescence correlation spectroscopy” Langmuir 34 25 7346-7354 (2018) [ https://doi.org/10.1021/acs.langmuir.8b00312 ]

39.     A.W. Long and A.L. Ferguson* “Rational design of patchy colloids via landscape engineering” Mol. Syst. Des. Eng. 3 1 49-65 (2018) [ http://dx.doi.org/10.1039/C7ME00077D ]

→ Invited submission to the 2018 Emerging Investigators issue
→ Selected for inside front cover image
→ Selected by journal as winner of RSC MSDE Emerging Investigator Award
→ Awarded the Institution of Chemical Engineers 2018/19 Junior Moulton Medal

32.     R.A. Mansbach and A.L. Ferguson* “Control of the hierarchical assembly of π-conjugated optoelectronic peptides by pH and flow” Org. Biomol. Chem. 15 26 5484-5502 (2017)
[ http://dx.doi.org/10.1039/C7OB00923B ]

→ Invited submission for “Peptide Materials” special issue
→ Selected as 2017 HOT Article in Organic and Biomolecular Chemistry
→ Featured as the cover article of Organic and Biomolecular Chemistry 15 26 (2017)

31.     J. Wang, M. Gayatri, and A.L. Ferguson* “Mesoscale simulation and machine learning of asphaltene aggregation phase behavior and molecular assembly landscapes” J. Phys. Chem. B 121 18 4923-4944 (2017)
[ http://dx.doi.org/10.1021/acs.jpcb.7b02574 ]

29.     R.A. Mansbach and A.L. Ferguson* “Coarse-grained molecular simulation of the hierarchical self-assembly of π-conjugated optoelectronic peptides” J. Phys. Chem. B 121 7 1684–1706 (2017)
[ http://dx.doi.org/10.1021/acs.jpcb.6b10165 ]

26.     J. Wang and A.L. Ferguson* “Mesoscale simulation of asphaltene aggregation” J. Phys. Chem. B 120 32 8016-8035 (2016) [ http://dx.doi.org/10.1021/acs.jpcb.6b05925 ]

25.     A.W. Long, C.L. Phillips, E. Jankowski, and A.L. Ferguson* “Nonlinear machine learning and design of reconfigurable digital colloids” Soft Matter 12 7119-7135 (2016) [ http://dx.doi.org/10.1039/C6SM01156J ]

21.     B.A. Thurston, J.D. Tovar, and A.L. Ferguson* “Thermodynamics, morphology, and kinetics of early-stage self-assembly of π-conjugated oligopeptides” Mol. Sim. 42 12 955-975 (2016)
[ http://dx.doi.org/10.1080/08927022.2015.1125997 ]

18.     A.W. Long, J. Zhang, S. Granick, and A.L. Ferguson* “Machine learning assembly landscapes from particle tracking data” Soft Matter 11 8141-8153 (2015) [ http://dx.doi.org/10.1039/C5SM01981H ]

14.     B.D. Wall, Y. Zhou, S. Mei, H.A.M. Ardoña, A.L. Ferguson and J.D. Tovar “Variation of formal hydrogen bonding networks within electronically delocalized pi-conjugated oligopeptide nanostructures” Langmuir 30 (38) 11375–11385 (2014) [ http://www.dx.doi.org/10.1021/la501999g ]

12.     B.D. Wall, A.E. Zacca, A.M. Sanders, W.L. Wilson, A.L. Ferguson and J.D. Tovar “Supramolecular polymorphism: Tunable electronic interactions within pi-conjugated peptide nanostructures dictated by primary amino acid sequence” Langmuir 30 20 5946-5956 (2014) [ http://dx.doi.org/10.1021/la500222y ]

11.      A.W. Long and A.L. Ferguson* “Nonlinear machine learning of patchy colloid self-assembly mechanisms and pathways” J. Phys. Chem. B 118 15 4228-4244 (2014) [ http://dx.doi.org/10.1021/jp500350b ]